Locus 182

Sequence ID X_DroMel_CAF1
Location 641,863 – 642,002
Length 139
Max. P 0.976369
window285 window286 window287

overview

Window 5

Location 641,863 – 641,962
Length 99
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 78.14
Mean single sequence MFE -24.42
Consensus MFE -19.82
Energy contribution -20.35
Covariance contribution 0.53
Combinations/Pair 1.06
Mean z-score -2.71
Structure conservation index 0.81
SVM decision value 1.77
SVM RNA-class probability 0.976369
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 641863 99 + 22224390
GAAUUUUAGUGAAAUUCCUCAAAUUCCU-CCAAAAACCC-----CAAAAACAGGAACUGGUGGCUUCUCCUGGCUACCGUCUUCCUGGUGACCUUCGCCACCCGC
((((((.((.(.....))).))))))..-..........-----.......(((((.((((((((......))))))))..)))))((((.....))))...... ( -25.50)
>DroSec_CAF1 7472 91 + 1
GAAUUUUACUGAAAUUCCUC---------CCAAAAACCC-----CAAAAACAGGAACUGGUGGCUUCUUCUGGCCACCGUCUUCCUGGUGACCUUCGCCACACGC
(((((((...)))))))...---------..........-----.......(((((.((((((((......))))))))..)))))((((.....))))...... ( -26.50)
>DroSim_CAF1 9061 91 + 1
GAAUUUUACUGAAAUUCCUC---------CCAAAAACCC-----CAAAAACAGGAACUGGUGGCUUCUCCUGGCCACCGUCUUCCUGGUGACCUUCGCCACACGC
(((((((...)))))))...---------..........-----.......(((((.((((((((......))))))))..)))))((((.....))))...... ( -26.50)
>DroEre_CAF1 137 102 + 1
AAAAUGUACUGAAAUUCCUCCAAUUCCAACCAAAAACACGAA---AAAAACAGGAACUGGUGGCUCCUCCUGGCCACCGUCUUCCUGGUGACCUUCGCCACCCGC
......................................((((---.....((((((.((((((((......))))))))..))))))......))))........ ( -23.70)
>DroYak_CAF1 142 105 + 1
GAAAUGUACUGAAACUCAUCCCAUUCCUACCAAAAACACAAACUCAACAACAGGAACUGGUGGCUGCUGCUGGCCACCGUCUUCCUGGUGACCUUCGCCACCCGC
(.((((...((.....))...)))).)........................(((((.((((((((......))))))))..)))))((((.....))))...... ( -24.40)
>DroAna_CAF1 127 93 + 1
--AUUCC----CCACUCCUCUGACUCCU-CUGAAUUCUC-----CUCGGACAGGAACUGGGGUCUCCUUCUGGCCACCGUCUUCCUGAUCACCUUUGCCACCCGA
--.....----.........(((....(-((((......-----.)))))((((((.(((((((.......)))).)))..)))))).))).............. ( -19.90)
>consensus
GAAUUUUACUGAAAUUCCUC__AUUCCU_CCAAAAACCC_____CAAAAACAGGAACUGGUGGCUUCUCCUGGCCACCGUCUUCCUGGUGACCUUCGCCACCCGC
...................................................(((((.((((((((......))))))))..)))))((((.....))))...... (-19.82 = -20.35 +   0.53) 

alignment

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secondary structure

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dotplot

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Window 6

Location 641,863 – 641,962
Length 99
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 78.14
Mean single sequence MFE -30.92
Consensus MFE -21.39
Energy contribution -21.92
Covariance contribution 0.53
Combinations/Pair 1.06
Mean z-score -1.47
Structure conservation index 0.69
SVM decision value 0.66
SVM RNA-class probability 0.814900
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 641863 99 - 22224390
GCGGGUGGCGAAGGUCACCAGGAAGACGGUAGCCAGGAGAAGCCACCAGUUCCUGUUUUUG-----GGGUUUUUGG-AGGAAUUUGAGGAAUUUCACUAAAAUUC
...((((((....))))))(((((...(((.((........)).)))..))))).....((-----..((((((.(-((...))).))))))..))......... ( -27.80)
>DroSec_CAF1 7472 91 - 1
GCGUGUGGCGAAGGUCACCAGGAAGACGGUGGCCAGAAGAAGCCACCAGUUCCUGUUUUUG-----GGGUUUUUGG---------GAGGAAUUUCAGUAAAAUUC
....(((((....)))))((((((...((((((........))))))..))))))...(((-----..(((((...---------..)))))..)))........ ( -31.60)
>DroSim_CAF1 9061 91 - 1
GCGUGUGGCGAAGGUCACCAGGAAGACGGUGGCCAGGAGAAGCCACCAGUUCCUGUUUUUG-----GGGUUUUUGG---------GAGGAAUUUCAGUAAAAUUC
....(((((....)))))((((((...((((((........))))))..))))))...(((-----..(((((...---------..)))))..)))........ ( -31.60)
>DroEre_CAF1 137 102 - 1
GCGGGUGGCGAAGGUCACCAGGAAGACGGUGGCCAGGAGGAGCCACCAGUUCCUGUUUUU---UUCGUGUUUUUGGUUGGAAUUGGAGGAAUUUCAGUACAUUUU
(((((((((....))))))(((((...((((((........))))))..)))))......---..)))........((((((((.....))))))))........ ( -33.40)
>DroYak_CAF1 142 105 - 1
GCGGGUGGCGAAGGUCACCAGGAAGACGGUGGCCAGCAGCAGCCACCAGUUCCUGUUGUUGAGUUUGUGUUUUUGGUAGGAAUGGGAUGAGUUUCAGUACAUUUC
...((((((....))))))..(((((((..((((((((((((..........))))))))).)))..)))))))....((((((...((.....))...)))))) ( -34.40)
>DroAna_CAF1 127 93 - 1
UCGGGUGGCAAAGGUGAUCAGGAAGACGGUGGCCAGAAGGAGACCCCAGUUCCUGUCCGAG-----GAGAAUUCAG-AGGAGUCAGAGGAGUGG----GGAAU--
............(((.(((........))).))).........(((((.(((((((((...-----(......)..-.)))..))).))).)))----))...-- ( -26.70)
>consensus
GCGGGUGGCGAAGGUCACCAGGAAGACGGUGGCCAGGAGAAGCCACCAGUUCCUGUUUUUG_____GGGUUUUUGG_AGGAAU__GAGGAAUUUCAGUAAAAUUC
....(((((....)))))((((((...((((((........))))))..)))))).................................................. (-21.39 = -21.92 +   0.53) 

alignment

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secondary structure

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dotplot

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Window 7

Location 641,888 – 642,002
Length 114
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 79.59
Mean single sequence MFE -32.83
Consensus MFE -15.30
Energy contribution -16.27
Covariance contribution 0.97
Combinations/Pair 1.15
Mean z-score -2.35
Structure conservation index 0.47
SVM decision value 0.25
SVM RNA-class probability 0.651706
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 641888 114 + 22224390
CCUCCAAAAACCCCAAAAACAGGAACUGGUGGCUUCUCCUGGCUACCGUCUUCCUGGUGACCUUCGCCACCCGCUUCUAUAAGGUCACCGAGCCGGAUCACAUAUGGUAACUGA
...................(((..((((((((((......)))))))((..(((((((((((((.((.....))......))))))))))....)))..))....)))..))). ( -34.30)
>DroPse_CAF1 11651 109 + 1
-----AAAAAUCUCUCUUCCAGGCAUUGGUGGAUCCUACUGGCAUCCGUGUUCCUCAUUACUUUUGCCACUCGCUUCUACAAGGUGACCGAACCGGAUCACAUCUGGUAAGGCA
-----................((((..(((((((((....)).))))(((.....))).)))..))))..((((((.....))))))((..(((((((...)))))))..)).. ( -29.30)
>DroSec_CAF1 7492 111 + 1
---CCAAAAACCCCAAAAACAGGAACUGGUGGCUUCUUCUGGCCACCGUCUUCCUGGUGACCUUCGCCACACGCUUCUAUAAGGUCACCGAACCGGACCACAUAUGGUAACUGA
---.........((......(((((.((((((((......))))))))..)))))(((((((((.((.....))......))))))))).....))((((....))))...... ( -37.30)
>DroSim_CAF1 9081 111 + 1
---CCAAAAACCCCAAAAACAGGAACUGGUGGCUUCUCCUGGCCACCGUCUUCCUGGUGACCUUCGCCACACGCUUCUAUAAGGUCACCGAACCGGAUCACAUAUGGUAACUGA
---................(((..((((((((((......)))))))((..(((((((((((((.((.....))......))))))))))....)))..))....)))..))). ( -36.60)
>DroAna_CAF1 146 114 + 1
CCUCUGAAUUCUCCUCGGACAGGAACUGGGGUCUCCUUCUGGCCACCGUCUUCCUGAUCACCUUUGCCACCCGAUUCUACAAGGUCACCGAACCGGAUCACAUUUGGUAAGUGG
..(((((.......)))))((((((.(((((((.......)))).)))..))))))....(((((((((...(((((.....(((......)))))))).....))))))).)) ( -30.70)
>DroPer_CAF1 11651 109 + 1
-----CAAAAUCUCUCUUCCAGGCAUUGGUGGAUCUUACUGGCAUCCGUGUUCCUCAUUACCUUUGCCACUCGCUUCUACAAGGUGACCGAACCGGAUCACAUCUGGUAAGGCA
-----................((((..(((((((((....)).))))(((.....))).)))..))))..((((((.....))))))((..(((((((...)))))))..)).. ( -28.80)
>consensus
___CCAAAAACCCCAAAAACAGGAACUGGUGGCUCCUACUGGCCACCGUCUUCCUGAUGACCUUCGCCACACGCUUCUACAAGGUCACCGAACCGGAUCACAUAUGGUAACUGA
...................(((((..(((.((((......)))).)))...))))).(((((((................)))))))(((...)))((((....))))...... (-15.30 = -16.27 +   0.97) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:20 2006